To be honest, I think shield penetration only makes sense if the missile is only able to penetrate enough to hit the arm holding the shield, and only if you hit the right spots, but I don't think it's doable with the module system.
It'd also make sense if throwing spears/jarids/throwing lances could hit the shielding arm with weaker shields as well, but that's opening up another can of worms.
At least the damage is greatly reduced whenever a missile goes through a shield.